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International Workshop on DNA-Based Computers

DNA 2003: DNA Computing pp 19–31Cite as

Chemical Switching and Molecular Logic in Fluorescent-Labeled M-DNA

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Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2943))

Abstract

M-DNA is a complex formed between duplex DNA and divalent metal ions at approximately pH 8.5. 30 base pair linear duplexes were prepared with fluorescein attached to one end, and various electron acceptors at the other. Quenching of the fluorescence emission from fluorescein by the acceptor molecules was observed under conditions corresponding to M-DNA, but not for B-DNA. For the case of anthraquinone as the acceptor, the quenching, which is ascribed to an electron transfer process, was blocked by chemical reduction (NaBH4) of anthraquinone to the dihydroanthraquinone which is not an electron acceptor. Upon the reoxidation of the dihydroanthraquinone by exposure to oxygen the quenching was restored. Quenching of fluorescein fluorescence was also observed in a 90 base pair Y-branched duplex in which rhodamine or anthraquinone were attached to one or two of the remaining arms. Thus the electron transfer process is not impeded by the presence of a junction in the duplex, contrary to results previously reported for B-DNA samples. Again the fluorescein fluorescence could be modulated by reduction of the anthraquinone group in the Y-branched duplexes, mimicking a simple chemical switch. A number of molecular logic functions are demonstrated in M-DNA by considering various chemical inputs, with the level of observed quenching serving as the observed output. Therefore M-DNA may have extraordinary potential for the development of nano-electronic devices.

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Authors and Affiliations

  1. Department of Biochemistry, University of Saskatchewan, 107 Wiggins Rd., Saskatoon, SK, S7N 5E5, Canada

    Shawn D. Wettig, Grant A. Bare, Ryan J. S. Skinner & Jeremy S. Lee

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  1. Shawn D. Wettig
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  2. Grant A. Bare
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  3. Ryan J. S. Skinner
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  4. Jeremy S. Lee
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Editor information

Editors and Affiliations

  1. Department of Chemistry, New York University, 10003, New York, NY, USA

    Junghuei Chen

  2. Department of Computer Science, Duke University, Durham, NC, USA

    John Reif

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© 2004 Springer-Verlag Berlin Heidelberg

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Wettig, S.D., Bare, G.A., Skinner, R.J.S., Lee, J.S. (2004). Chemical Switching and Molecular Logic in Fluorescent-Labeled M-DNA. In: Chen, J., Reif, J. (eds) DNA Computing. DNA 2003. Lecture Notes in Computer Science, vol 2943. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24628-2_3

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  • DOI: https://doi.org/10.1007/978-3-540-24628-2_3

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-20930-0

  • Online ISBN: 978-3-540-24628-2

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